Index

A

add_substrate() (autoprot.analysis.functional.KSEA method) adjust_p() (in module autoprot.analysis.stat_test) annotate() (autoprot.analysis.functional.KSEA method) annotate_df() (autoprot.analysis.functional.KSEA method) annotate_phosphosite() (in module autoprot.preprocessing.annotation) auto_run() (autoprot.analysis.clustering.HCA method) (autoprot.analysis.clustering.KMeans method) AutoPCA (class in autoprot.analysis.PCA) autoprot.analysis.functional module autoprot.analysis.qc module autoprot.analysis.stat_test module autoprot.analysis.stats module autoprot.preprocessing.annotation module

autoprot.preprocessing.data_handling module autoprot.preprocessing.filtering module autoprot.preprocessing.imputation module autoprot.preprocessing.normalization module autoprot.preprocessing.transformation module autoprot.visualization.annotation module autoprot.visualization.basic module autoprot.visualization.qc module

B

bar_load() (autoprot.analysis.PCA.AutoPCA method)

bi_plot() (autoprot.analysis.PCA.AutoPCA method) boxplot() (in module autoprot.visualization.basic)

C

calculate_iBAQ() (in module autoprot.preprocessing.transformation) charge_plot() (in module autoprot.visualization.qc) cleaning() (in module autoprot.preprocessing.filtering) clear_manual_substrates() (autoprot.analysis.functional.KSEA method) cohen_d() (in module autoprot.analysis.stat_test)

collapse_rows() (in module autoprot.preprocessing.transformation) corr_comp() (autoprot.analysis.PCA.AutoPCA method) corr_map() (in module autoprot.visualization.basic) correlogram() (in module autoprot.visualization.basic) count_mod_aa() (in module autoprot.visualization.qc) cyclic_loess() (in module autoprot.preprocessing.normalization)

D

dima() (in module autoprot.preprocessing.imputation)

dimethyl_labeling_efficieny() (in module autoprot.analysis.qc) download_from_ftp() (in module autoprot.preprocessing.data_handling)

E

edm() (in module autoprot.analysis.stats) enrichment_specifity() (in module autoprot.analysis.qc)

exp_semi_col() (in module autoprot.preprocessing.transformation) expand_site_table() (in module autoprot.preprocessing.transformation)

F

fetch_from_pride() (in module autoprot.preprocessing.data_handling) filter_loc_prob() (in module autoprot.preprocessing.filtering) filter_seq_cov() (in module autoprot.preprocessing.filtering)

filter_vv() (in module autoprot.preprocessing.filtering) find_nclusters() (autoprot.analysis.clustering.HCA method) (autoprot.analysis.clustering.KMeans method)

G

get_kinase_overview() (autoprot.analysis.functional.KSEA method) get_subcellular_loc() (in module autoprot.preprocessing.annotation)

go_analysis() (in module autoprot.analysis.functional) go_annot() (in module autoprot.preprocessing.annotation)

H

HCA (class in autoprot.analysis.clustering)

I

i_lolli_plot() (in module autoprot.visualization.annotation) i_mirror_lolli_plot() (in module autoprot.visualization.annotation) icharge_plot() (in module autoprot.visualization.qc) icount_mod_aa() (in module autoprot.visualization.qc) ima_plot() (in module autoprot.visualization.basic)

imp_min_prob() (in module autoprot.preprocessing.imputation) imp_seq() (in module autoprot.preprocessing.imputation) intensity_rank() (in module autoprot.visualization.basic) isequence_logo() (in module autoprot.visualization.annotation) isty_count_plot() (in module autoprot.visualization.qc) ivolcano() (in module autoprot.visualization.basic)

K

KMeans (class in autoprot.analysis.clustering)

KSEA (class in autoprot.analysis.functional) ksea() (autoprot.analysis.functional.KSEA method)

L

limma() (in module autoprot.analysis.stat_test) loading_plot() (autoprot.analysis.PCA.AutoPCA method)

loess() (in module autoprot.analysis.stats) log() (in module autoprot.preprocessing.transformation) log_int_plot() (in module autoprot.visualization.basic)

M

ma_plot() (in module autoprot.visualization.basic) make_cluster() (autoprot.analysis.clustering.HCA method) (autoprot.analysis.clustering.KMeans method) make_linkage() (autoprot.analysis.clustering.HCA method) make_psm() (in module autoprot.analysis.stats) make_sim_score() (in module autoprot.preprocessing.transformation) mean_sd_plot() (in module autoprot.visualization.basic) merge_semi_cols() (in module autoprot.preprocessing.transformation) miss_analysis() (in module autoprot.analysis.qc) missed_cleavages() (in module autoprot.analysis.qc) module autoprot.analysis.functional autoprot.analysis.qc autoprot.analysis.stat_test autoprot.analysis.stats autoprot.preprocessing.annotation autoprot.preprocessing.data_handling autoprot.preprocessing.filtering autoprot.preprocessing.imputation autoprot.preprocessing.normalization autoprot.preprocessing.transformation autoprot.visualization.annotation autoprot.visualization.basic autoprot.visualization.qc

motif_annot() (in module autoprot.preprocessing.annotation)

N

norm_to_prot() (in module autoprot.preprocessing.normalization)

P

pair_plot() (autoprot.analysis.PCA.AutoPCA method) plot_enrichment() (autoprot.analysis.functional.KSEA method) plot_traces() (in module autoprot.visualization.basic) plot_volcano() (autoprot.analysis.functional.KSEA method)

prob_plot() (in module autoprot.visualization.basic) ptm_lolli_plot() (in module autoprot.visualization.annotation) ptm_mirror_lolli_plot() (in module autoprot.visualization.annotation) pval_hist() (in module autoprot.visualization.basic)

Q

quantile_norm() (in module autoprot.preprocessing.normalization)

R

rank_prod() (in module autoprot.analysis.stat_test) ratio_plot() (in module autoprot.visualization.basic) read_csv() (in module autoprot.preprocessing.data_handling) remove_non_quant() (in module autoprot.preprocessing.filtering)

replot_totals() (autoprot.visualization.basic.UpSetGrouped method) return_enrichment() (autoprot.analysis.functional.KSEA method) return_kinase_substrate() (autoprot.analysis.functional.KSEA method) return_load() (autoprot.analysis.PCA.AutoPCA method) return_score() (autoprot.analysis.PCA.AutoPCA method)

S

score_plot() (autoprot.analysis.PCA.AutoPCA method) scree() (autoprot.analysis.PCA.AutoPCA method) sequence_logo() (in module autoprot.visualization.annotation)

SILAC_labeling_efficiency() (in module autoprot.analysis.qc) sty_count_plot() (in module autoprot.visualization.qc) styling_helper() (autoprot.visualization.basic.UpSetGrouped method)

T

tmt6plex_labeling_efficiency() (in module autoprot.analysis.qc) to_canonical_ps() (in module autoprot.preprocessing.annotation)

to_csv() (in module autoprot.preprocessing.data_handling) ttest() (in module autoprot.analysis.stat_test)

U

UpSetGrouped (class in autoprot.visualization.basic)

V

venn_diagram() (in module autoprot.visualization.basic) vis_psites() (in module autoprot.visualization.annotation)

volcano() (in module autoprot.visualization.basic) vsn() (in module autoprot.preprocessing.normalization)